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Tuesday, August 26, 2008

The Trichoplax Genome

Trichoplax adherens is a very simple animal that moves about on surfaces like a gigantic amoeba and ingests any food that it flows over. There are thought to be several species of Trichoplax in addition to Trichoplax adherens.

Because this is such a simple and unusual animal it has been assigned its own phylum, Placozoa with Trichoplax as the only genus.1

The diagram below is copied from Syed and Shierwater (2002). It shows clearly that Trichoplax adhaerens is a true metazoan with an upper (dorsal) epithelial layer, a lower (ventral) epithelial layer, and an internal layer of contractile fiber cells. There are at least four cell types, not counting the egg and sperm cells that have been reported by others.

Where does Trichoplax fit in the evolution of animals? Clearly, the lineage leading to modern Trichoplax must have diverged very early in animal evolution. This is why Trichoplax is often (incorrectly) referred to as a "primitive animal", or a "living fossil." (See Ryan Gregory's discussion of this terminology at: Kudos on the placozoan genome!.)

The exact branch point is hotly disputed. Did the ancestors of Trichoplax split off before or after the sponges (Porifera) or the Cnideria (jelleyfish, hydras, corals)? Is the modern form of Trichoplax the ancestral form or is it a derived and simplified version of a more complex animal?

Trichoplax adherens has six chromosomes and a total genome size of about 98 × 106 base pairs (98 Mb). The authors identified 11,514 protein-encoding genes. Because the genome sequence is "only" 98% complete, it wasn't possible to reconstruct entire chromosomes and the association between the sequenced genome and particular chromosomes is impossible to establish due to the absence of genetic studies on Trichoplax (no linkage maps).

The genome is smaller than that of the green alga Chlamydomonas reinhardtii with a genome of 121 Mb and about 15,000 genes [The Genome of Chlamydomonas reinhardtii]. On the other hand, the Trichoplax genome is larger than that of other single-cell organisms such as the protist Giardia lamblia (12 Mb, ~6500 genes) [The Giardia lamblia Genome].

The Trichoplax genome is almost the same size as the C. elegans (nematode) genome at 97 Mb but C. elegans is thought to have more than 15,000 genes. Drosophila melanogaster at 180 Mb has ~16,000 genes and mammals have a genome of 3,300 Mb and 20,000 genes.

About 90% of the Trichoplax genes are present in other animals and the intron positions of the Trichoplax are mostly identical to those in other animals [Junk in Your Genome: Intron Size and Distribution]. This is powerful evidence that the phylum Placozoa belongs in the animal kingdom.

Srivastava et al. constructed a phylogenetic tree using 104 highly conserved genes from species whose complete genomes are available in the sequence databases. The tree (below) shows that the Trichoplax lineage branches after sponges (represented by Amphimedon queenslandica) but before cnidarians (Hydra magnipapillata). The result are not compatible with trees constructed using mitochondrial sequences or ribosomal RNA sequences but that's not too surprising. Mitochondrial DNA and ribosomal RNA sequences are often not reliable for this kind of work.

The conclusion is that Placozoa and most metazoans diverged about 600 million years ago but sponges diverged even earlier.

1. It isn't unusual to create separate phyla for organisms with distinct body plans but you wouldn't know that from the criticisms leveled at Stephen Jay Gould when he published Wonderful Life [Science and Philosophy Book Club: Wonderful Life]. Incidentally, in The Ancestor's Tale Dawkins readily accepts that Trichoplax adherens may be the sole species in the phylum Placozoa.

[Image Credit: The photograph of Trichoplax is from metamorphnet. That website also has some wonderful movies of Trichoplax.

7 comments
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"The result are not compatible with trees constructed using mitochondrial sequences or ribosomal RNA sequences but that's not too surprising. Mitochondrial DNA and ribosomal RNA sequences are often not reliable for this kind of work"

I'd say that definitely there were morphological reasons to consider this basal, but otherwise there wasn't much morphological reason for a particular affinity to the eumetazoa. They could be the mos basal metazoa; also, the possiblity that placozoans are simplified sponges is not discarded by this new data, since porifera may be paraphyletic, including the clade placozoa+eumetazoa.

Even genome wide-comparisons are likely to change if the taxon sampling is poor. Including intermediate forms can (and will!) change the structure of the tree.

In this sense I commend the work for having included a choanoflagellate, but that's about it. The calcisponges are not there: only a demosponge. The deuterostome is..."human"! The protostomes are a snail and fruitfly, and both cnidarians are anthozoans (as far as I know). The ctenophores, as usual, are the elephant in the room: they usually have this thing: in molecular studies, they POOF! DISAPPEAR!!!

There is no evident morphological signal. Placozoa are similar to some poriferan and cnidarian larvae, simpler if anything. It is usually the case that mithochondrial and ribosomal genes have better taxon sampling. I would take genes that have a good taxonomic sampling more seriously. We'll see what happens: There is still much "bizarre that needs sequencing!!!!

Hexactinlellid (silicatous)sponges, THOSE are the ones missing, crucial to this case (their spicules are the oldest in the fossil record)

Despite the shortcomings of taxon sampling the genome-wide comparisons results are still a good possibility according to morphology and have basically confirming the morphologically most parsimonious assumption, that Placozoa are basal metazoa. Those aspects will for sure be maintained when taxon sampling is improved.

The more specific questions may still find new answers with better data.

BTW, of course, some sponges DO have fibrilar contractile cells; Actually the actin-myosin contractile apparatus is a pre-metacellular innovation.

It's a good post but has one flaw. The assumption "coding sequence = gene" is quite wrong. If a gene is the sequence responsible for a heritable trait, then there are a large number of RNAi genes that we know little about. Several, for example, are involved in malignancy, and that certainly is a heritable trait.

It's a good post but has one flaw. The assumption "coding sequence = gene" is quite wrong.

I have never made that assumption as anyone who reads my opinions on genes and genomes would know.

If a gene is the sequence responsible for a heritable trait, then there are a large number of RNAi genes that we know little about. Several, for example, are involved in malignancy, and that certainly is a heritable trait.

I'm well aware of the existence of genes whose product is RNA. Been teaching that for over thirty years. We've known about small regulatory RNAs for almost as long.

The question is not whether genes for small regulatory RNAs exist, it's whether there are a lot of them. I don't think there are lots of them, certainly not enough to make a significant difference in the number of genes.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

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My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.